Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

comparison tool_dependencies.xml @ 8:aafba27d2c8a draft default tip

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planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
author mvdbeek
date Sun, 25 Oct 2015 18:51:24 -0400
parents 5f56355f5f7c
children
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7:5f56355f5f7c 8:aafba27d2c8a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="ascp" version="3"> 3 <package name="ascp" version="3">
4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="perl" version="5.18.1">
7 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 8 </package>
6 <package name="ncbi_vdb" version="2.5.2"> 9 <package name="ncbi_vdb" version="2.5.2">
7 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package> 11 </package>
9 <package name="ngs_sdk" version="1.1.3"> 12 <package name="ngs_sdk" version="1.1.3">
10 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 14 </package>
12 <package name="perl" version="5.18.1">
13 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="sra_toolkit" version="2.5.2"> 15 <package name="sra_toolkit" version="2.5.2">
16 <install version="1.0"> 16 <install version="1.0">
17 <actions> 17 <actions>
18 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> 18 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
19 <action type="set_environment_for_install"> 19 <action type="set_environment_for_install">
20 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="perl" version="5.18.1" />
22 </repository>
20 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 23 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
21 <package name="ncbi_vdb" version="2.5.2" /> 24 <package name="ncbi_vdb" version="2.5.2" />
22 </repository> 25 </repository>
23 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu"> 26 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
24 <package name="ngs_sdk" version="1.1.3" /> 27 <package name="ngs_sdk" version="1.1.3" />
25 </repository> 28 </repository>
26 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
27 <package name="perl" version="5.18.1" />
28 </repository>
29 </action> 29 </action>
30 <action type="autoconf"> 30 <action type="shell">
31 --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build 31 ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
32 </action> 32 </action>
33 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action> 33 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
34 <action type="make_install" /> 34 <action type="make_install" />
35 <action type="set_environment"> 35 <action type="set_environment">
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>